Cargando…

ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures

BACKGROUND: Periodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms h...

Descripción completa

Detalles Bibliográficos
Autores principales: Hrabe, Thomas, Godzik, Adam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021314/
https://www.ncbi.nlm.nih.gov/pubmed/24766872
http://dx.doi.org/10.1186/1471-2105-15-119
_version_ 1782316217248251904
author Hrabe, Thomas
Godzik, Adam
author_facet Hrabe, Thomas
Godzik, Adam
author_sort Hrabe, Thomas
collection PubMed
description BACKGROUND: Periodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins. RESULTS: ConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families. CONCLUSIONS: The ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org.
format Online
Article
Text
id pubmed-4021314
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-40213142014-05-28 ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures Hrabe, Thomas Godzik, Adam BMC Bioinformatics Methodology Article BACKGROUND: Periodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins. RESULTS: ConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families. CONCLUSIONS: The ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org. BioMed Central 2014-04-27 /pmc/articles/PMC4021314/ /pubmed/24766872 http://dx.doi.org/10.1186/1471-2105-15-119 Text en Copyright © 2014 Hrabe and Godzik; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology Article
Hrabe, Thomas
Godzik, Adam
ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures
title ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures
title_full ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures
title_fullStr ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures
title_full_unstemmed ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures
title_short ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures
title_sort console: using modularity of contact maps to locate solenoid domains in protein structures
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021314/
https://www.ncbi.nlm.nih.gov/pubmed/24766872
http://dx.doi.org/10.1186/1471-2105-15-119
work_keys_str_mv AT hrabethomas consoleusingmodularityofcontactmapstolocatesolenoiddomainsinproteinstructures
AT godzikadam consoleusingmodularityofcontactmapstolocatesolenoiddomainsinproteinstructures